How to distort effects with equirectangular projection
Lens flare depends on the orientation of the lens you are looking through in relation to the light source so it cannot be rendered into a panoramic image that is then viewed as if the orientation of the camera would be changing.

It would have to be an effect generated while viewing the image. So the answer seems to be:

No. There is no way to compensate for this at the stage where you are making the panoramic image. 

It should be done at the stage where the image is viewed.